The end of the episode, inside Peter's brain, is a reference to The Twilight Zone (1959) episode Time Enough at Last (1959)
First time Peter stubs his knee and responds with his signature "sssss...aaaaahhhh"
While Peter plays the theme to The X-Files (1993) solo on the piano, the arrangement on the soundtrack is impossible to play without three hands.
A caricature of Seth McFarlane appears in the background next to Mary Tyler Moore as she throws her hat in the air.